50 results on '"Daehan Lee"'
Search Results
2. Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila
- Author
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Bumsik Cho, Sang-Ho Yoon, Daewon Lee, Ferdinand Koranteng, Sudhir Gopal Tattikota, Nuri Cha, Mingyu Shin, Hobin Do, Yanhui Hu, Sue Young Oh, Daehan Lee, A. Vipin Menon, Seok Jun Moon, Norbert Perrimon, Jin-Wu Nam, and Jiwon Shim
- Subjects
Science - Abstract
How the Drosophila lymph gland hemocytes develop and are regulated at a single-cell level is unclear. Here, the authors use single-cell RNA sequencing to show heterogeneity of developing hemocytes in the lymph gland and how they react to wasp infestation, and compare hemocytes from two independent origins.
- Published
- 2020
- Full Text
- View/download PDF
3. A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans.
- Author
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Yuehui Zhao, Lijiang Long, Jason Wan, Shweta Biliya, Shannon C Brady, Daehan Lee, Akinade Ojemakinde, Erik C Andersen, Fredrik O Vannberg, Hang Lu, and Patrick T McGrath
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Genetics ,QH426-470 - Abstract
Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking. In this report, we study the genetic basis of adaptation of two strains of C. elegans to laboratory food sources using competition experiments on a panel of 89 recombinant inbred lines (RIL). Unexpectedly, we identified a single RIL with higher relative fitness than either of the parental strains. This strain also displayed a novel behavioral phenotype, resulting in higher propensity to explore bacterial lawns. Using bulk-segregant analysis and short-read resequencing of this RIL, we mapped the change in exploration behavior to a spontaneous, complex rearrangement of the rcan-1 gene that occurred during construction of the RIL panel. We resolved this rearrangement into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1 calcipressin gene, which has been implicated as a causal gene for Down syndrome. The genomic rearrangement in rcan-1 creates two complete and two truncated versions of the rcan-1 coding region, with a variety of modified 5' and 3' non-coding regions. While most copy-number variations (CNVs) are thought to act by increasing expression of duplicated genes, these changes to rcan-1 ultimately result in the reduction of its whole-body expression due to changes in the upstream regions. By backcrossing this rearrangement into a common genetic background to create a near isogenic line (NIL), we demonstrate that both the competitive advantage and exploration behavioral changes are linked to this complex genetic variant. This NIL strain does not phenocopy a strain containing an rcan-1 loss-of-function allele, which suggests that the residual expression of rcan-1 is necessary for its fitness effects. Our results demonstrate how colonization of new environments, such as those encountered in the laboratory, can create evolutionary pressure to modify gene function. This evolutionary mismatch can be resolved by an unexpectedly complex genetic change that simultaneously duplicates and diversifies a gene into two uniquely regulated genes. Our work shows how complex rearrangements can act to modify gene expression in ways besides increased gene dosage.
- Published
- 2020
- Full Text
- View/download PDF
4. Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations
- Author
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Tim A Crombie, Stefan Zdraljevic, Daniel E Cook, Robyn E Tanny, Shannon C Brady, Ye Wang, Kathryn S Evans, Steffen Hahnel, Daehan Lee, Briana C Rodriguez, Gaotian Zhang, Joost van der Zwagg, Karin Kiontke, and Erik C Andersen
- Subjects
Caenorhabditis elegans ,Hawaii ,Caenorhabditis oiwi ,genetic diversity ,niche ,admixture ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral genetic diversity in the C. elegans species before human influence.
- Published
- 2019
- Full Text
- View/download PDF
5. An Experimental Analysis of Active Pitch Control for an Assault Amphibious Vehicle Considering Waterjet-Hydrofoil Interaction Effect
- Author
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Daehan Lee, Sanggi Ko, Jongyeol Park, Yong Cheol Kwon, Shin Hyung Rhee, Myungjun Jeon, and Tae Hyung Kim
- Subjects
amphibious vehicle ,motor-driven waterjet system ,pitch motion control ,seakeeping tests ,Naval architecture. Shipbuilding. Marine engineering ,VM1-989 ,Oceanography ,GC1-1581 - Abstract
The present study aims to reduce the pitch motion of an assault amphibious vehicle system in seaways by waterjet impeller revolution rate control. A series of seakeeping tests were performed in a towing tank with a 1/4.5-scale model. This vehicle is manufactured as a box-shaped hull, and since an appendage that generates lift force is attached, the amount of change in pitch motion is large according to the forward speed. For pitch motion reduction, the impeller revolution rate and resultant pitch moment were controlled through a proportional-integral-derivative controller. Improvements in seakeeping performance were examined in both regular and irregular conditions by the model tests in terms of root mean square of pitch motion. The tuned controller decreased pitch motion by more than 60%.
- Published
- 2021
- Full Text
- View/download PDF
6. The genetic basis of natural variation in a phoretic behavior
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Daehan Lee, Heeseung Yang, Jun Kim, Shannon Brady, Stefan Zdraljevic, Mostafa Zamanian, Heekyeong Kim, Young-ki Paik, Leonid Kruglyak, Erik C. Andersen, and Junho Lee
- Subjects
Science - Abstract
Nematodes use a characteristic set of movements, called nictation, to hitchhike on more mobile animals. Here, Lee et al. identify a genetic locus in the nematode Caenorhabditis elegans that underlies nictation and contributes to successful hitchhiking, but at expense of reduced offspring production.
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- 2017
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7. Discovery of genomic intervals that underlie nematode responses to benzimidazoles.
- Author
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Mostafa Zamanian, Daniel E Cook, Stefan Zdraljevic, Shannon C Brady, Daehan Lee, Junho Lee, and Erik C Andersen
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
Parasitic nematodes impose a debilitating health and economic burden across much of the world. Nematode resistance to anthelmintic drugs threatens parasite control efforts in both human and veterinary medicine. Despite this threat, the genetic landscape of potential resistance mechanisms to these critical drugs remains largely unexplored. Here, we exploit natural variation in the model nematodes Caenorhabditis elegans and Caenorhabditis briggsae to discover quantitative trait loci (QTL) that control sensitivity to benzimidazoles widely used in human and animal medicine. High-throughput phenotyping of albendazole, fenbendazole, mebendazole, and thiabendazole responses in panels of recombinant lines led to the discovery of over 15 QTL in C. elegans and four QTL in C. briggsae associated with divergent responses to these anthelmintics. Many of these QTL are conserved across benzimidazole derivatives, but others show drug and dose specificity. We used near-isogenic lines to recapitulate and narrow the C. elegans albendazole QTL of largest effect and identified candidate variants correlated with the resistance phenotype. These QTL do not overlap with known benzimidazole target resistance genes from parasitic nematodes and present specific new leads for the discovery of novel mechanisms of nematode benzimidazole resistance. Analyses of orthologous genes reveal conservation of candidate benzimidazole resistance genes in medically important parasitic nematodes. These data provide a basis for extending these approaches to other anthelmintic drug classes and a pathway towards validating new markers for anthelmintic resistance that can be deployed to improve parasite disease control.
- Published
- 2018
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- View/download PDF
8. Nictation Assays for Caenorhabditis and Other Nematodes
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Daehan Lee, Harksun Lee, Myung-kyu Choi, Sungsu Park, and Junho Lee
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Biology (General) ,QH301-705.5 - Abstract
Nictation is a dauer-specific standing and waving behavior of the nematodes including Caenorhabditis species. Nictation enhances the capability of free-living nematodes to hitchhike to other animals as well as parasitic nematodes to infect their hosts. However, lack of an assay for this behavior has made it difficult to elucidate its underlying regulatory mechanisms and related genetic pathways. We have developed nictation assays that enable the quantification of the nictation behavior of individuals and groups of worms. Gauze assay is less quantitative but is an easier way to observe nictation behavior in plates with plenty of dauers. The micro-dirt chip made from PDMS mold is a more sophisticated method to quantify the nictation behavior. Nictation can be quantified on a micro-dirt chip either by measuring the average nictating time of individual dauers or by the fraction of nictating worms in a given dauer population.
- Published
- 2015
- Full Text
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9. Glial expression of a steroidogenic enzyme underlies natural variation in hitchhiking behavior.
- Author
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Heeseung Yang, Daehan Lee, Heekyeong Kim, Cook, Daniel E., Young-Ki Paik, Andersen, Erik C., and Junho Lee
- Subjects
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CAENORHABDITIS elegans , *HITCHHIKING , *GENETIC variation , *GENOME-wide association studies , *ENZYMES - Abstract
Phoresy is an interspecies interaction that facilitates spatial dispersal by attaching to a more mobile species. Hitchhiking species have evolved specific traits for physical contact and successful phoresy, but the regulatory mechanisms involved in such traits and their evolution are largely unexplored. The nematode Caenorhabditis elegans displays a hitchhiking behavior known as nictation during its stress-induced developmental stage. Dauer-specific nictation behavior has an important role in natural C. elegans populations, which experience boom-and-bust population dynamics. In this study, we investigated the nictation behavior of 137 wild C. elegans strains sampled throughout the world. We identified species-wide natural variation in nictation and performed a genome-wide association mapping. We show that the variants in the promoter of nta-1, encoding a putative steroidogenic enzyme, underlie differences in nictation. This difference is due to the changes in nta-1 expression in glial cells, which implies that glial steroid metabolism regulates phoretic behavior. Population genetic analysis and geographic distribution patterns suggest that balancing selection maintained two nta-1 haplotypes that existed in ancestral C. elegans populations. Our findings contribute to further understanding of the molecular mechanism of species interaction and the maintenance of genetic diversity within natural populations. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
10. Accumulative Charge Separation in a Modular Quaterpyridine Bridging Ligand Platform and Multielectron Transfer Photocatalysis of π-Linked Dinuclear Ir(III)–Re(I) Complex for CO2 Reduction
- Author
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Daehan Lee, Min Su Choe, Hyung Joo Lee, Jae Yoon Shin, Chul Hoon Kim, Ho-Jin Son, and Sang Ook Kang
- Subjects
Inorganic Chemistry ,Physical and Theoretical Chemistry - Published
- 2023
11. daf-42 is an evolutionarily young gene essential for dauer development in Caenorhabditis elegans
- Author
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Daisy S Lim, Jun Kim, Wonjoo Kim, Nari Kim, Sang-Hee Lee, Daehan Lee, and Junho Lee
- Subjects
Genetics - Abstract
Under adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauer endures unfavorable environments and interacts with host animals to access favorable environments, thus playing a critical role in survival. Here, we report that in Caenorhabditis elegans, daf-42 is essential for development into the dauer stage, as the null mutant of daf-42 exhibited a “no viable dauer” phenotype in which no viable dauers were obtained in any dauer-inducing conditions. Long-term time lapse microscopy of synchronized larvae revealed that daf-42 is involved in developmental changes from the pre-dauer L2d stage to the dauer stage. daf-42 encodes large, disordered proteins of various sizes that are expressed in and secreted from the seam cells within a narrow time window shortly before the molt into dauer stage. Transcriptome analysis showed that the transcription of genes involved in larval physiology and dauer metabolism are highly affected by the daf-42 mutation. Contrary to the notion that essential genes that control the life and death of an organism may well be conserved across diverse species, daf-42 is an evolutionarily young gene conserved only in the Caenorhabditis genus. Our study shows that dauer formation is a vital process that is controlled not only by conserved genes but also by newly emerged genes, providing important insights into evolutionary mechanisms.
- Published
- 2023
12. daf-42is an evolutionarily young gene essential for dauer development inCaenorhabditis elegans
- Author
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Daisy S. Lim, Jun Kim, Wonjoo Kim, Nari Kim, Sang-Hee Lee, Daehan Lee, and Junho Lee
- Abstract
Under adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauer endures unfavorable environments and interacts with host animals to access favorable environments, thus playing a critical role in survival. Here, we report that inCaenorhabditis elegans,daf-42is essential for development into the dauer stage, as the null mutant ofdaf-42exhibited a “no viable dauer” phenotype in which no viable dauers were obtained in any dauer-inducing conditions. Long-term time lapse microscopy of synchonized larvae revealed thatdaf-42is involved in developmental changes from the pre-dauer L2d stage to the dauer stage.daf-42encodes large, disordered proteins of various sizes that are expressed in and secreted from the seam cells within a narrow time window shortly before the molt into dauer stage. Transcriptome analysis showed that the transcription of genes involved in larval physiology and dauer metabolism are highly affected by thedaf-42 mutation. Contrary to the notion that essential genes that control the life and death of an organism may well be conserved across diverse species,daf-42is an evolutionarily young gene conserved only in theCaenorhabditisgenus. Our study shows that dauer formation is a vital process that is controlled not only by conserved genes but also by newly emerged genes, providing important insights into evolutionary mechanisms.
- Published
- 2023
13. Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands
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Clayton M. Dilks, Daniel E. Cook, T. A. Crombie, Claire M. Buchanan, Kathryn S. Evans, Michael Ailion, Daehan Lee, Stefan Zdraljevic, L. A. Stinson, Paul Battlay, Erik C. Andersen, Robyn E. Tanny, Kathryn A. Hodgins, N. M. Roberto, and Gaotian Zhang
- Subjects
Islands ,Genetic diversity ,education ,Niche ,Genetic Variation ,Biology ,Balancing selection ,biology.organism_classification ,Genome ,Hawaii ,Evolutionary biology ,Temperate climate ,Caenorhabditis ,Genetics ,Animals ,Adaptation ,Caenorhabditis elegans ,Ecology, Evolution, Behavior and Systematics ,Local adaptation - Abstract
The nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Wild C. elegans have been isolated from both temperate and tropical climates, where they feed on bacteria associated with decomposing plant material. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. The high genetic diversity found there suggests that: (1) the origin of the species lies in Hawaii or the surrounding Pacific Rim; and (2) the ancestral niche of the species is likely similar to the Hawaiian niche. A recent study of the Hawaiian niche found that genetically distinct groups appeared to correlate with elevation and temperature, but the study had a limited sample size. To better characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three-year period, measured various environmental parameters at each sampling site, and whole-genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche is moderately moist native forests at high elevations (500 to 1500 meters) where temperatures are cool (15 to 20°C). We measured levels of genetic diversity and differentiation among Hawaiian strains and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyperdivergent regions, which are likely maintained by balancing selection and enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and a possible genetic basis for this adaptation.
- Published
- 2022
14. Natural genetic variation in the pheromone production ofC. elegans
- Author
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Daehan Lee, Bennett W. Fox, Diana C. F. Palomino, Oishika Panda, Francisco J. Tenjo, Emily J. Koury, Kathryn S. Evans, Lewis Stevens, Pedro R. Rodrigues, Aiden R. Kolodziej, Frank C. Schroeder, and Erik C. Andersen
- Abstract
From bacterial quorum sensing to human language, communication is essential for social interactions. Nematodes produce and sense pheromones to communicate among individuals and respond to environmental changes. These signals are encoded by different types and mixtures of ascarosides, whose modular structures further enhance the diversity of this nematode pheromone language. Interspecific and intraspecific differences in this ascaroside pheromone language have been described previously, but the genetic basis and molecular mechanisms underlying the variation remain largely unknown. Here, we analyzed natural variation in the production of 44 ascarosides across 95 wildCaenorhabditis elegansstrains using high-performance liquid chromatography coupled to high-resolution mass spectrometry (HPLC-HRMS). By cross-analyzing genomes andexo-metabolomes of wild strains, we discovered quantitative trait loci (QTL) that underlie the natural differences in pheromone bouquet composition. Fine mapping of the QTL further uncovered associations between mitochondrial metabolism and pheromone production. Our findings demonstrate how natural genetic variation in core metabolic pathways can affect the production of social signals.
- Published
- 2022
15. Secondary Coordination Effect on Monobipyridyl Ru(II) Catalysts in Photochemical CO2 Reduction: Effective Proton Shuttle of Pendant Brønsted Acid/Base Sites (OH and N(CH3)2) and Its Mechanistic Investigation
- Author
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Sang Ook Kang, Yunjeong Seo, S.J. Choi, Ho-Jin Son, Jin-Ook Baeg, Changhyun Back, Min Su Choe, and Daehan Lee
- Subjects
Inorganic Chemistry ,chemistry.chemical_compound ,Bipyridine ,Coordination sphere ,chemistry ,Ligand ,Hydrogen bond ,Formate ,Physical and Theoretical Chemistry ,Selectivity ,Brønsted–Lowry acid–base theory ,Medicinal chemistry ,Catalysis - Abstract
While the incorporation of pendant Bronsted acid/base sites in the secondary coordination sphere is a promising and effective strategy to increase the catalytic performance and product selectivity in organometallic catalysis for CO2 reduction, the control of product selectivity still faces a great challenge. Herein, we report two new trans(Cl)-[Ru(6-X-bpy)(CO)2Cl2] complexes functionalized with a saturated ethylene-linked functional group (bpy = 2,2'-bipyridine; X = -(CH2)2-OH or -(CH2)2-N(CH3)2) at the ortho(6)-position of bpy ligand, which are named Ru-bpyOH and Ru-bpydiMeN, respectively. In the series of photolysis experiments, compared to nontethered case, the asymmetric attachment of tethering ligand to the bpy ligand led to less efficient but more selective formate production with inactivation of CO2-to-CO conversion route during photoreaction. From a series of in situ FTIR analyses, it was found that the Ru-formate intermediates are stabilized by a highly probable hydrogen bonding between pendent proton donors (-diMeN+H or -OH) and the oxygen atom of metal-bound formate (RuI-OCHO···H-E-(CH2)2-, E = O or diMeN+). Under such conformation, the liberation of formate from the stabilized RuI-formate becomes less efficient compared to the nontethered case, consequently lowering the CO2-to-formate conversion activities during photoreaction. At the same time, such stabilization of Ru-formate species prevents the dehydration reaction route (η1-OCHO → η1-COOH on Ru metal) which leads toward the generation of Ru-CO species (key intermediate for CO production), eventually leading to the reduction of CO2-to-CO conversion activity.
- Published
- 2021
16. Photochemical CO2-to-Formate/CO Conversion Catalyzed by Half-Metallocene Ir(III) Catalyst and Its Mechanistic Investigation
- Author
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Ho-Jin Son, Daehan Lee, Sang Ook Kang, So-Yoen Kim, Min Su Choe, S.J. Choi, Kyutai Park, and Chul Hoon Kim
- Subjects
Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Organic Chemistry ,Formate ,Physical and Theoretical Chemistry ,Photochemistry ,Metallocene ,Catalysis - Published
- 2021
17. A Hybrid Ru(II)/TiO2 Catalyst for Steadfast Photocatalytic CO2 to CO/Formate Conversion Following a Molecular Catalytic Route
- Author
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Hyun Seok Lee, So-Yoen Kim, Min Su Choe, Ho-Jin Son, Daehan Lee, Sang Ook Kang, Chul Hoon Kim, S.J. Choi, and Changhyun Back
- Subjects
Inorganic Chemistry ,chemistry.chemical_compound ,Monomer ,chemistry ,Polymer chemistry ,Photocatalysis ,Homogeneous catalysis ,Formate ,Electron donor ,Physical and Theoretical Chemistry ,Fourier transform infrared spectroscopy ,Catalysis - Abstract
Herein, we employed a molecular Ru(II) catalyst immobilized onto TiO2 particulates of (4,4'-Y2-bpy)RuII(CO)2Cl2 (RuP; Y = CH2PO(OH)2), as a hybrid catalyst system to secure the efficient and steady catalytic activity of a molecular bipyridyl Ru(II)-complex-based photocatalytic system for CO2 reduction. From a series of operando FTIR spectrochemical analyses, it was found that the TiO2-fixed molecular Ru(II) complex leads to efficient stabilization of the key monomeric intermediate, RuII-hydride (LRuII(H)(CO)2Cl), and suppresses the formation of polymeric Ru(II) complex (-(L(CO)2Ru-Ru(CO)2L)n-), which is a major deactivation product produced during photoreaction via the Ru-Ru dimeric route. Active promotion of the monomeric catalytic route in a hetero-binary system (IrPS + TiO2/RuP) that uses TiO2-bound Ru(II) complex as reduction catalyst led to highly increased activity as well as durability of photocatalytic behavior with respect to the homogeneous catalysis of free Ru(II) catalyst (IrPS + Ru(II) catalyst). This catalytic strategy produced maximal turnover numbers (TONs) of >4816 and >2228, respectively, for CO and HCOO- production in CO2-saturated N,N-dimethylformamide (DMF)/TEOA (16.7 vol % TEOA) solution containing a 0.1 M sacrificial electron donor.
- Published
- 2021
18. Natural genetic variation in the pheromone production of C. elegans.
- Author
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Daehan Lee, Fox, Bennett W., Fajardo Palomino, Diana, Panda, Oishika, Tenjo, Francisco J., Koury, Emily J., Evans, Kathryn S., Stevens, Lewis, Rodrigues, Pedro R., Kolodziej, Aiden R., Schroeder, Frank C., and Andersen, Erik C.
- Subjects
- *
CAENORHABDITIS elegans , *GENETIC variation , *HIGH performance liquid chromatography , *PHEROMONES , *MODULAR construction - Abstract
From bacterial quorum sensing to human language, communication is essential for social interactions. Nematodes produce and sense pheromones to communicate among individuals and respond to environmental changes. These signals are encoded by different types and mixtures of ascarosides, whose modular structures further enhance the diversity of this nematode pheromone language. Interspecific and intraspecific differences in this ascaroside pheromone language have been described previously, but the genetic basis and molecular mechanisms underlying the variation remain largely unknown. Here, we analyzed natural variation in the production of 44 ascarosides across 95 wild Caenorhabditis elegans strains using high-performance liquid chromatography coupled to high-resolution mass spectrometry. We discovered wild strains defective in the production of specific subsets of ascarosides (e.g., the aggregation pheromone icas#9) or short- and medium-chain ascarosides, as well as inversely correlated patterns between the production of two major classes of ascarosides. We investigated genetic variants that are significantly associated with the natural differences in the composition of the pheromone bouquet, including rare genetic variants in key enzymes participating in ascaroside biosynthesis, such as the peroxisomal 3-ketoacyl-CoA thiolase, daf-22, and the carboxylesterase cest-3. Genome-wide association mappings revealed genomic loci harboring common variants that affect ascaroside profiles. Our study yields a valuable dataset for investigating the genetic mechanisms underlying the evolution of chemical communication. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
19. Electron Injection Process of Porphyrin Dye into a Heterogeneous TiO2/Re(I) Photocatalyst
- Author
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Sang Ook Kang, Min Su Choe, S.J. Choi, Ho-Jin Son, Daehan Lee, Jae Yoon Shin, Chul Hoon Kim, Chyongjin Pac, and So-Yoen Kim
- Subjects
Materials science ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Photochemistry ,01 natural sciences ,Porphyrin ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,chemistry.chemical_compound ,General Energy ,chemistry ,Electron injection ,Scientific method ,Photocatalysis ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
We now report full details of the collisional ET process at the interface between the solvated porphyrin dye (a representative molecular dye) and heterogeneous TiO2 particles (a well-defined n-type...
- Published
- 2021
20. Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans
- Author
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Daniel E. Cook, Erik C. Andersen, L. Ryan Baugh, Stefan Zdraljevic, Ye Wang, Matthew V. Rockman, Robyn E. Tanny, Amy K. Webster, Rojin Chirakar, Christian Braendle, Timothy A. Crombie, Daehan Lee, Lewis Stevens, Marie-Anne Félix, and Mark G. Sterken
- Subjects
0303 health sciences ,Genetic diversity ,education.field_of_study ,Ecology ,Population ,Selfing ,Outcrossing ,Biology ,biology.organism_classification ,Balancing selection ,Caenorhabditis ,03 medical and health sciences ,0302 clinical medicine ,Effective population size ,Genetic drift ,Evolutionary biology ,Life Science ,Laboratory of Nematology ,education ,Laboratorium voor Nematologie ,030217 neurology & neurosurgery ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology - Abstract
Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing decreases the effective population size, effective recombination rate and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genus Caenorhabditis, selfing has evolved at least three times, and all three species, including the model organism Caenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wild C. elegans strains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found between Caenorhabditis species that diverged millions of years ago. These results provide an example of how species can avoid the evolutionary dead end associated with selfing.
- Published
- 2021
21. Quasi-Reflectionless Differential Phase Shifter with Arbitrary Prescribed Group Delay and Flat Phase Difference
- Author
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Girdhari Chaudhary, Daehan Lee, Muhammad A. Chaudary, and Yongchae Jeong
- Published
- 2022
22. An atlas of gene expression variation across the Caenorhabditis elegans species
- Author
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Gaotian Zhang, Nicole M. Roberto, Daehan Lee, Steffen R. Hahnel, and Erik C. Andersen
- Abstract
Phenotypic variation in diverse organism-level traits have been studied in Caenorhabditis elegans wild strains, but differences in gene expression and the underlying variation in regulatory mechanisms are largely unknown. Here, we use natural variation in gene expression to connect genetic variants to differences in organismal- level traits, including drug and toxicant responses. We performed transcriptomic analysis on 207 genetically distinct C. elegans wild strains to study natural regulatory variation of gene expression. Using this massive dataset, we performed genome-wide association mappings to investigate the genetic basis underlying gene expression variation and revealed complex genetic architectures. We found a large collection of hotspots enriched for expression quantitative trait loci across the genome. We further used mediation analysis to understand how gene expression variation could underlie organism-level phenotypic variation for a variety of complex traits. These results reveal the natural diversity in gene expression and possible regulatory mechanisms in this keystone model organism, highlighting the promise of gene expression variation in shaping phenotypic diversity.
- Published
- 2022
23. Group Delay Analysis Approach for Quasi-Reflectionless Power Divider With Flat Phase Difference
- Author
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Girdhari Chaudhary, Daehan Lee, and Yongchae Jeong
- Published
- 2021
24. Secondary Coordination Effect on Monobipyridyl Ru(II) Catalysts in Photochemical CO
- Author
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Changhyun, Back, Yunjeong, Seo, Sunghan, Choi, Min Su, Choe, Daehan, Lee, Jin-Ook, Baeg, Ho-Jin, Son, and Sang Ook, Kang
- Abstract
While the incorporation of pendant Brønsted acid/base sites in the secondary coordination sphere is a promising and effective strategy to increase the catalytic performance and product selectivity in organometallic catalysis for CO
- Published
- 2021
25. An Experimental Analysis of Active Pitch Control for an Assault Amphibious Vehicle Considering Waterjet-Hydrofoil Interaction Effect
- Author
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Tae Hyung Kim, Shin Hyung Rhee, Myungjun Jeon, Jongyeol Park, Sanggi Ko, Yong Cheol Kwon, and Daehan Lee
- Subjects
Naval architecture. Shipbuilding. Marine engineering ,VM1-989 ,Ocean Engineering ,Seakeeping ,GC1-1581 ,motor-driven waterjet system ,Oceanography ,Root mean square ,Impeller ,amphibious vehicle ,pitch motion control ,Pitch control ,Control theory ,Hull ,seakeeping tests ,Reduction (mathematics) ,Towing ,Water Science and Technology ,Civil and Structural Engineering ,Marine engineering ,Mathematics - Abstract
The present study aims to reduce the pitch motion of an assault amphibious vehicle system in seaways by waterjet impeller revolution rate control. A series of seakeeping tests were performed in a towing tank with a 1/4.5-scale model. This vehicle is manufactured as a box-shaped hull, and since an appendage that generates lift force is attached, the amount of change in pitch motion is large according to the forward speed. For pitch motion reduction, the impeller revolution rate and resultant pitch moment were controlled through a proportional-integral-derivative controller. Improvements in seakeeping performance were examined in both regular and irregular conditions by the model tests in terms of root mean square of pitch motion. The tuned controller decreased pitch motion by more than 60%.
- Published
- 2021
26. First Opinion: Sicily in the Aquarium: A Father, Daughter, and the Inspiring Story of Jeanne Power.
- Author
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Daehan Lee
- Subjects
AQUARIUMS ,REFUGEE camps - Published
- 2023
27. A Hybrid Ru(II)/TiO
- Author
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Min Su, Choe, Sunghan, Choi, So-Yoen, Kim, Changhyun, Back, Daehan, Lee, Hyun Seok, Lee, Chul Hoon, Kim, Ho-Jin, Son, and Sang Ook, Kang
- Abstract
Herein, we employed a molecular Ru(II) catalyst immobilized onto TiO
- Published
- 2021
28. A Novel Gene Underlies Bleomycin-Response Variation in Caenorhabditis elegans
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Daniel E. Cook, Erik C. Andersen, Ye Wang, Stefan Zdraljevic, Shannon C. Brady, Karol W. Bisaga, Robyn E. Tanny, and Daehan Lee
- Subjects
Genetics ,0303 health sciences ,biology ,ved/biology ,Strain (biology) ,ved/biology.organism_classification_rank.species ,respiratory system ,Quantitative trait locus ,biology.organism_classification ,Bleomycin ,respiratory tract diseases ,3. Good health ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,chemistry ,Genetic linkage ,Allele ,Model organism ,Gene ,030217 neurology & neurosurgery ,Caenorhabditis elegans ,030304 developmental biology - Abstract
Bleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organism Caenorhabditis elegans to identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain (N2) and a wild strain (CB4856). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines, and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene (scb-1) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function of scb-1 between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance.
- Published
- 2019
29. Development of a new tool for objective risk assessment and comparative analysis at coastal waters
- Author
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Daehan Lee, Hong-Hoon Lee, and Inchul Kim
- Subjects
Geography ,Objective risk ,Traffic risk ,Risk assessment ,Environmental planning - Abstract
The International Association of Marine Aids to Navigation and Lighthouse Authorities (IALA) introduced maritime traffic risk assessment models such as Waterway Risk Assessment Program and Ports an...
- Published
- 2019
30. Uncertainty assessment of outdoor free-running model tests for maneuverability analysis of a damaged surface combatant
- Author
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Jongyeol Park, Daehan Lee, Gyukpo Park, Shin Hyung Rhee, Jeonghwa Seo, and Hyeon Kyu Yoon
- Subjects
Environmental Engineering ,Ocean Engineering - Published
- 2022
31. Balancing selection maintains hyper-divergent haplotypes inC. elegans
- Author
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Daehan Lee, Ye Wang, Christian Braendle, Robyn E. Tanny, Matthew V. Rockman, Rojin Chirakar, Daniel E. Cook, Erik C. Andersen, L. Ryan Baugh, Lewis Stevens, Stefan Zdraljevic, Marie-Anne Félix, Mark G. Sterken, Timothy A. Crombie, and Amy K. Webster
- Subjects
Caenorhabditis ,education.field_of_study ,Genetic diversity ,Effective population size ,Genetic drift ,Evolutionary biology ,Population ,Selfing ,Outcrossing ,Biology ,education ,Balancing selection ,biology.organism_classification - Abstract
Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing significantly decreases the effective population size, effective recombination rate, and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genusCaenorhabditis, selfing has evolved at least three times and all three species, including in the model organismCaenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossingCaenorhabditisspecies are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wildC. elegansstrains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of theC. elegansreference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response, and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found betweenCaenorhabditisspecies that diverged millions of years ago. These results provide an example for how species can avoid the evolutionary “dead end” associated with selfing.
- Published
- 2020
32. A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans
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Lijiang Long, Daehan Lee, Jason Wan, Fredrik O. Vannberg, Hang Lu, Shannon C. Brady, Erik C. Andersen, Akinade Ojemakinde, Yuehui Zhao, Patrick T. McGrath, and Shweta Biliya
- Subjects
Male ,Evolutionary Genetics ,Cancer Research ,Nematoda ,Inbred Strains ,Gene Expression ,Social Sciences ,Artificial Gene Amplification and Extension ,QH426-470 ,Polymerase Chain Reaction ,Database and Informatics Methods ,0302 clinical medicine ,Loss of Function Mutation ,Gene Duplication ,Coding region ,Psychology ,Inbreeding ,Genetics (clinical) ,Genomic organization ,Genetics ,0303 health sciences ,Intracellular Signaling Peptides and Proteins ,Eukaryota ,Animal Models ,Genomics ,DNA-Binding Proteins ,Experimental Organism Systems ,Sequence Analysis ,Research Article ,Bioinformatics ,Biology ,Research and Analysis Methods ,Genome Complexity ,Gene dosage ,Evolution, Molecular ,03 medical and health sciences ,Model Organisms ,Animals ,Allele ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,Molecular Biology Techniques ,Gene ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Alleles ,030304 developmental biology ,Phenocopy ,Evolutionary Biology ,Behavior ,Human evolutionary genetics ,Organisms ,Biology and Life Sciences ,Computational Biology ,Evolutionary pressure ,Invertebrates ,13. Climate action ,Exploratory Behavior ,Animal Studies ,Caenorhabditis ,Genetic Fitness ,Sequence Alignment ,030217 neurology & neurosurgery - Abstract
Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking. In this report, we study the genetic basis of adaptation of two strains of C. elegans to laboratory food sources using competition experiments on a panel of 89 recombinant inbred lines (RIL). Unexpectedly, we identified a single RIL with higher relative fitness than either of the parental strains. This strain also displayed a novel behavioral phenotype, resulting in higher propensity to explore bacterial lawns. Using bulk-segregant analysis and short-read resequencing of this RIL, we mapped the change in exploration behavior to a spontaneous, complex rearrangement of the rcan-1 gene that occurred during construction of the RIL panel. We resolved this rearrangement into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1 calcipressin gene, which has been implicated as a causal gene for Down syndrome. The genomic rearrangement in rcan-1 creates two complete and two truncated versions of the rcan-1 coding region, with a variety of modified 5’ and 3’ non-coding regions. While most copy-number variations (CNVs) are thought to act by increasing expression of duplicated genes, these changes to rcan-1 ultimately result in the reduction of its whole-body expression due to changes in the upstream regions. By backcrossing this rearrangement into a common genetic background to create a near isogenic line (NIL), we demonstrate that both the competitive advantage and exploration behavioral changes are linked to this complex genetic variant. This NIL strain does not phenocopy a strain containing an rcan-1 loss-of-function allele, which suggests that the residual expression of rcan-1 is necessary for its fitness effects. Our results demonstrate how colonization of new environments, such as those encountered in the laboratory, can create evolutionary pressure to modify gene function. This evolutionary mismatch can be resolved by an unexpectedly complex genetic change that simultaneously duplicates and diversifies a gene into two uniquely regulated genes. Our work shows how complex rearrangements can act to modify gene expression in ways besides increased gene dosage., Author summary Evolution acts on genetic variants that modify phenotypes that increase the likelihood of staying alive and passing on these genetic changes to subsequent generations (i.e. fitness). There is general interest in understanding the types of genetic variants that can increase fitness in specific environments. One route that fitness can be increased is through changes in behavior, such as finding new food sources. Here, we identify a spontaneous genetic change that increases exploration behavior and fitness of animals in laboratory environments. Interestingly, this genetic change is not a simple genetic change that deletes or changes the sequence of a protein product, but rather a complex structural variant that simultaneously duplicates the rcan-1 gene and also modifies its expression in a number of tissues. Our work demonstrates how a complex structural change can duplicate a gene, modify the DNA control regions that determine its cellular sites of action, and confer a fitness advantage that could lead to its spread in a population.
- Published
- 2020
33. Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila
- Author
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Hobin Do, Ferdinand Koranteng, Daehan Lee, Sang-Ho Yoon, Jiwon Shim, A. Vipin Menon, Seok Jun Moon, Nuri Cha, Jin Wu Nam, Norbert Perrimon, Mingyu Shin, Sue Young Oh, Daewon Lee, Yanhui Hu, Sudhir Gopal Tattikota, and Bumsik Cho
- Subjects
0301 basic medicine ,Cellular immunity ,Myeloid ,Hemocytes ,Lymphoid Tissue ,Science ,Wasps ,General Physics and Astronomy ,Ectoparasitic Infestations ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Host-Parasite Interactions ,Blood cell ,Animals, Genetically Modified ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,medicine ,Animals ,Cell Lineage ,RNA-Seq ,lcsh:Science ,Myelopoiesis ,Multidisciplinary ,Innate immune system ,Haematopoietic stem cells ,Gene Expression Profiling ,Hematopoietic stem cell ,Cell Differentiation ,General Chemistry ,Cell biology ,Hematopoiesis ,Innate immune cells ,Haematopoiesis ,030104 developmental biology ,medicine.anatomical_structure ,Drosophila melanogaster ,Differentiation ,lcsh:Q ,Single-Cell Analysis ,Transcriptome ,030217 neurology & neurosurgery - Abstract
The Drosophila lymph gland, the larval hematopoietic organ comprised of prohemocytes and mature hemocytes, has been a valuable model for understanding mechanisms underlying hematopoiesis and immunity. Three types of mature hemocytes have been characterized in the lymph gland: plasmatocytes, lamellocytes, and crystal cells, which are analogous to vertebrate myeloid cells, yet molecular underpinnings of the lymph gland hemocytes have been less investigated. Here, we use single-cell RNA sequencing to comprehensively analyze heterogeneity of developing hemocytes in the lymph gland, and discover previously undescribed hemocyte types including adipohemocytes, stem-like prohemocytes, and intermediate prohemocytes. Additionally, we identify the developmental trajectory of hemocytes during normal development as well as the emergence of the lamellocyte lineage following active cellular immunity caused by wasp infestation. Finally, we establish similarities and differences between embryonically derived- and larval lymph gland hemocytes. Altogether, our study provides detailed insights into the hemocyte development and cellular immune responses at single-cell resolution., How the Drosophila lymph gland hemocytes develop and are regulated at a single-cell level is unclear. Here, the authors use single-cell RNA sequencing to show heterogeneity of developing hemocytes in the lymph gland and how they react to wasp infestation, and compare hemocytes from two independent origins.
- Published
- 2020
34. Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations
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Ye Wang, Erik C. Andersen, Daehan Lee, Karin Kiontke, Gaotian Zhang, Briana C. Rodriguez, Daniel E. Cook, Joost van der Zwaag, Steffen Hahnel, Kathryn S. Evans, Stefan Zdraljevic, Shannon C. Brady, Timothy A. Crombie, and Robyn E. Tanny
- Subjects
0106 biological sciences ,0301 basic medicine ,QH301-705.5 ,Science ,ved/biology.organism_classification_rank.species ,education ,Population ,Niche ,Genomics ,Biology ,010603 evolutionary biology ,01 natural sciences ,Hawaii ,General Biochemistry, Genetics and Molecular Biology ,Gene flow ,03 medical and health sciences ,Caenorhabditis oiwi ,Biology (General) ,Allele ,Caenorhabditis elegans ,Model organism ,030304 developmental biology ,Ecological niche ,0303 health sciences ,Genetic diversity ,education.field_of_study ,General Immunology and Microbiology ,ved/biology ,General Neuroscience ,Haplotype ,genetic diversity ,General Medicine ,biology.organism_classification ,Caenorhabditis ,niche ,030104 developmental biology ,Nematode ,Habitat ,Evolutionary biology ,admixture ,Medicine ,human activities ,geographic locations - Abstract
Recent efforts to understand the natural niche of the keystone model organismCaenorhabditis eleganshave suggested that this species is cosmopolitan and associated with rotting vegetation and fruits. However, most of the strains isolated from nature have low genetic diversity likely because recent chromosome-scale selective sweeps contain alleles that increase fitness in human-associated habitats. Strains from the Hawaii Islands are highly divergent from non-Hawaiian strains. This result suggests that Hawaiian strains might contain ancestral genetic diversity that was purged from most non-Hawaiian strains by the selective sweeps. To characterize the genetic diversity and niche of HawaiianC. elegans, we sampled across the Hawaiian Islands and isolated 100 newC. elegansstrains. We found thatC. elegansstrains are not associated with any one substrate but are found in cooler climates at high elevations. These Hawaiian strains are highly diverged compared to the rest of the global population. Admixture analysis identified 11 global populations, four of which are from Hawaii. Surprisingly, one of the Hawaiian populations shares recent ancestry with non-Hawaiian populations, including portions of globally swept haplotypes. This discovery provides the first evidence of gene flow between Hawaiian and non-Hawaiian populations. Most importantly, the high levels of diversity observed in Hawaiian strains might represent the complex patterns of ancestral genetic diversity in theC. elegansspecies before human influence.
- Published
- 2019
35. Author response: Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations
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Joost van der Zwagg, Briana C. Rodriguez, Daniel E. Cook, Stefan Zdraljevic, Shannon C. Brady, Karin Kiontke, Gaotian Zhang, Robyn E. Tanny, Daehan Lee, Erik C. Andersen, Timothy A. Crombie, Ye Wang, Kathryn S. Evans, and Steffen Hahnel
- Subjects
Genetic diversity ,biology ,Evolutionary biology ,Sampling (statistics) ,biology.organism_classification ,Caenorhabditis elegans - Published
- 2019
36. Regulation of a hitchhiking behavior by neuronal insulin and TGF-β signaling in the nematode Caenorhabditis elegans
- Author
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Daehan Lee, Junho Lee, Harksun Lee, Daisy S. Lim, and Nari Kim
- Subjects
0301 basic medicine ,Nervous system ,medicine.medical_specialty ,Nematode caenorhabditis elegans ,medicine.medical_treatment ,Period (gene) ,Biophysics ,Biology ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Downregulation and upregulation ,Transforming Growth Factor beta ,Internal medicine ,medicine ,Animals ,Insulin ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,Molecular Biology ,Neurons ,fungi ,Cell Biology ,Cell biology ,Insulin receptor ,030104 developmental biology ,Endocrinology ,medicine.anatomical_structure ,p21-Activated Kinases ,biology.protein ,Epistasis ,Signal transduction ,030217 neurology & neurosurgery ,Signal Transduction - Abstract
Free-living nematode Caenorhabditis elegans exhibits various behaviors to adapt to the fluctuating environment. When early larvae of C. elegans experience the harsh environmental condition, they develop to an alternative developmental stage called dauer, which shows nictation, a stage-specific waving behavior. Nictation enables dauers to attach to more mobile animals, which helps them disperse to other habitats beyond physical barriers. However, underlying molecular mechanisms that regulate nictation behavior are largely unknown. In this study, we show that insulin signaling and transforming growth beta (TGF-β) signaling, the two major parallel signaling pathways that mediate dauer development, are involved in the regulation of dauer-specific nictation behavior. Genetic analysis revealed that downregulation of insulin signaling enhanced nictation behavior. Heat-shock induced rescue experiments showed that the action period of the insulin signaling is before dauer formation. Surprisingly, lowering of TGF-β signaling inhibited the normal performance of nictation, suggesting that TGF-β signaling acts in an opposite way from that for dauer formation. Cell-specific rescue experiments revealed that two signaling pathways act in the nervous system and an epistasis experiment showed that TGF-β signaling is epistatic to insulin signaling. Taken together, we propose that the neuroendocrinal insulin signaling and TGF-β signaling regulate nictation behavior during development in response to environmental conditions.
- Published
- 2017
37. Selection and gene flow shape niche-associated variation in pheromone response
- Author
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Lise Frézal, Joost A. G. Riksen, John Wang, Erik C. Andersen, Jan E. Kammenga, Jung Chen Hsu, Frank C. Schroeder, Stefan Zdraljevic, Daniel E. Cook, Mark G. Sterken, Marie-Anne Félix, Christian Braendle, Daehan Lee, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre of Pharmacology and Toxicology, Hannover Medical School, Department of Ecology and Evolutionary Biology, Princeton University -Lewis-Sigler Institute for Integrative Genomics, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Gene Flow ,[SDV]Life Sciences [q-bio] ,Population ,Niche ,Biology ,Balancing selection ,Article ,Pheromones ,Gene flow ,03 medical and health sciences ,0302 clinical medicine ,Animals ,Life Science ,Allele ,Caenorhabditis elegans ,education ,Laboratorium voor Nematologie ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Ecology ,[SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,PE&RC ,Quorum sensing ,Evolutionary biology ,Sex pheromone ,Pheromone ,EPS ,Laboratory of Nematology ,030217 neurology & neurosurgery - Abstract
International audience; From quorum sensing in bacteria to pheromone signalling in social insects, chemical communication mediates interactions among individuals in local populations. In Caenorhabditis elegans, ascaroside pheromones can dictate local population density; high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated variation in pheromone receptor genes contributes to natural differences in pheromone responses. We identified putative loss-of-function deletions that impair duplicated pheromone receptor genes (srg-36 and srg-37), which were previously shown to be lost in population-dense laboratory cultures. A common natural deletion in srg-37 arose recently from a single ancestral population that spread throughout the world; this deletion underlies reduced pheromone sensitivity across the global C. elegans population. We found that many local populations harbour individuals with a wild-type or a deletion allele of srg-37, suggesting that balancing selection has maintained the recent variation in this pheromone receptor gene. The two srg-37 genotypes are associated with niche diversity underlying boom-and-bust population dynamics. We hypothesize that human activities likely contributed to the gene flow and balancing selection of srg-37 variation through facilitating the migration of species and providing a favourable niche for the recently arisen srg-37 deletion.
- Published
- 2019
38. A Novel Gene Underlies Bleomycin-Response Variation in
- Author
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Shannon C, Brady, Stefan, Zdraljevic, Karol W, Bisaga, Robyn E, Tanny, Daniel E, Cook, Daehan, Lee, Ye, Wang, and Erik C, Andersen
- Subjects
linkage mapping ,Antibiotics, Antineoplastic ,Polymorphism, Genetic ,C. elegans bleomycin ,QTL ,Quantitative Trait Loci ,Nuclear Proteins ,respiratory system ,Investigations ,respiratory tract diseases ,carbohydrates (lipids) ,Bleomycin ,Quantitative Trait, Heritable ,Drug Resistance, Neoplasm ,Animals ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,drug-response ,Population and Evolutionary Genetics - Abstract
Bleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organism Caenorhabditis elegans to identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain (N2) and a wild strain (CB4856). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines, and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene (scb-1) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function of scb-1 between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance.
- Published
- 2019
39. Selection and gene flow shape niche-associated copy-number variation of pheromone receptor genes
- Author
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John Wang, Christian Braendle, Frank C. Schroeder, Jan E. Kammenga, Daniel E. Cook, Marie-Anne Félix, Daehan Lee, Jung Chen Hsu, Lise Frézal, Mark G. Sterken, Joost A. G. Riksen, Erik C. Andersen, and Stefan Zdraljevic
- Subjects
Genetics ,0303 health sciences ,education.field_of_study ,Population ,Biology ,biology.organism_classification ,Gene flow ,03 medical and health sciences ,0302 clinical medicine ,Natural population growth ,Sex pheromone ,Pheromone ,Copy-number variation ,education ,030217 neurology & neurosurgery ,Caenorhabditis elegans ,030304 developmental biology ,Local adaptation - Abstract
From quorum sensing in bacteria to pheromone signaling in social insects, chemical communication mediates interactions among individuals in a local population. InCaenorhabditis elegans, ascaroside pheromones can dictate local population density, in which high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated copy-number variation (CNV) of pheromone receptor genes contributes to natural differences in pheromone responses. We found putative loss-of-function deletions that reduce copy number of duplicated pheromone receptor genes (srg-36 and srg-37), which were shown previously to be selected in population-dense laboratory cultures. A common natural deletion in the less functional copy (srg-37) arose from a single ancestral population that spread throughout the world and underlies reduced pheromone sensitivity across the globalC. eleganspopulation. This deletion is enriched in wild strains that were isolated from a rotting fruit niche, where proliferating populations are often found. Taken together, these results demonstrate that selection and gene flow together shape the copy number of pheromone receptor genes in naturalC. eleganspopulations to facilitate local adaptation to diverse niches.
- Published
- 2019
40. A beneficial genomic rearrangement creates multiple versions of calcipressin inC. elegans
- Author
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Hang Lu, Patrick T. McGrath, Shweta Biliya, Fredrik O. Vannberg, Erik C. Andersen, Daehan Lee, Shannon C. Brady, Jason Wan, and Yuehui Zhao
- Subjects
Phenocopy ,Genetics ,0303 health sciences ,Calcipressin ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Gene duplication ,Coding region ,Nanopore sequencing ,Allele ,Adaptation ,Gene ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Gene duplication is a major source of genetic novelty and evolutionary adaptation, providing a molecular substrate that can generate biological complexity and diversity (Ohno 1967, Taylor and Raes 2004). Despite an abundance of genomic evidence from extant organisms suggesting the importance of gene duplication, consensus about how they arise and functionally diversify is lacking (Innan and Kondrashov 2010). In the process of studying the adaptation of laboratory strains of C. elegans to new food sources, we identified a recombinant inbred line (RIL) with higher relative fitness and hyperactive exploration behavior compared to either parental strain. Using bulk-segregant analysis and short-read resequencing, we identified a de novo beneficial, complex rearrangement of the rcan-1 gene, which we resolved into five new unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1, which has been implicated as a causal gene for Down syndrome (Fuentes, Genesca et al. 2000). The genomic rearrangement in rcan-1 causes two complete and two truncated versions of the rcan-1 coding region, with a variety of modified promoter and 3’ regions, which ultimately reduce whole-body gene expression. This rearrangement does not phenocopy a loss-of-function allele, which indicates that the rearrangement was necessary for the observed fitness gains. Our results demonstrate that adaptation can occur through unexpectedly complex genetic changes that can simultaneously duplicate and diversify a gene, providing the molecular substrate for future evolutionary change.
- Published
- 2019
41. A nematode-specific gene underlies bleomycin-response variation in Caenorhabditis elegans
- Author
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Erik C. Andersen, Daehan Lee, Karol W. Bisaga, Ye Wang, Daniel E. Cook, Robyn E. Tanny, Stefan Zdraljevic, and Shannon C. Brady
- Subjects
Genetics ,0303 health sciences ,Candidate gene ,biology ,ved/biology ,ved/biology.organism_classification_rank.species ,Quantitative trait locus ,respiratory system ,biology.organism_classification ,3. Good health ,respiratory tract diseases ,carbohydrates (lipids) ,03 medical and health sciences ,0302 clinical medicine ,Genetic linkage ,030220 oncology & carcinogenesis ,Allele ,Association mapping ,Model organism ,Gene ,Caenorhabditis elegans ,030304 developmental biology - Abstract
Bleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organism Caenorhabditis elegans to identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain (N2) and a wild strain (CB4856). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene ( scb-1 ) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function of scb-1 between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance. Article summary We performed linkage mapping on a panel of recombinant lines generated between two genetically divergent strains of Caenorhabditis elegans and identified a bleomycin-response QTL. We generated CRISPR-Cas9 deletions and reciprocal allele-replacement strains for all six candidate genes across the QTL confidence interval. Deletions of one gene, H19N07.3 , caused increased bleomycin sensitivity in both divergent genetic backgrounds. This gene might act in stress responses and detoxification in nematodes. We further compared our linkage mapping to a genome-wide association mapping and showed that a rare expression variant in the CB4856 strain likely underlies bleomycin-response differences.
- Published
- 2019
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42. Discovery of genomic intervals that underlie nematode responses to benzimidazoles
- Author
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Stefan Zdraljevic, Erik C. Andersen, Daniel E. Cook, Shannon C. Brady, Daehan Lee, Junho Lee, and Mostafa Zamanian
- Subjects
0301 basic medicine ,Nematoda ,Drug Resistance ,Drug resistance ,Genome ,Drug Discovery ,Medicine and Health Sciences ,Anthelmintic ,Nematode Infections ,Caenorhabditis elegans ,Genetics ,Anthelmintics ,biology ,Drug discovery ,Organic Compounds ,Antinematodal Agents ,lcsh:Public aspects of medicine ,Eukaryota ,Animal Models ,Genomics ,3. Good health ,Chemistry ,Phenotypes ,Infectious Diseases ,Phenotype ,Experimental Organism Systems ,Physical Sciences ,medicine.drug ,Research Article ,Caenorhabditis briggsae ,Drug Research and Development ,lcsh:Arctic medicine. Tropical medicine ,lcsh:RC955-962 ,Quantitative Trait Loci ,Quantitative trait locus ,Research and Analysis Methods ,Albendazole ,03 medical and health sciences ,Model Organisms ,medicine ,Animals ,Humans ,Molecular Biology Techniques ,Linkage Mapping ,Molecular Biology ,Pharmacology ,Genome, Helminth ,Organic Chemistry ,Gene Mapping ,Public Health, Environmental and Occupational Health ,Chemical Compounds ,Organisms ,Biology and Life Sciences ,lcsh:RA1-1270 ,Fenbendazole ,biology.organism_classification ,Veterinary Parasitology ,Invertebrates ,030104 developmental biology ,Nematode ,Genetic Loci ,Caenorhabditis ,Benzimidazoles ,Parasitology ,Veterinary Science - Abstract
Parasitic nematodes impose a debilitating health and economic burden across much of the world. Nematode resistance to anthelmintic drugs threatens parasite control efforts in both human and veterinary medicine. Despite this threat, the genetic landscape of potential resistance mechanisms to these critical drugs remains largely unexplored. Here, we exploit natural variation in the model nematodes Caenorhabditis elegans and Caenorhabditis briggsae to discover quantitative trait loci (QTL) that control sensitivity to benzimidazoles widely used in human and animal medicine. High-throughput phenotyping of albendazole, fenbendazole, mebendazole, and thiabendazole responses in panels of recombinant lines led to the discovery of over 15 QTL in C. elegans and four QTL in C. briggsae associated with divergent responses to these anthelmintics. Many of these QTL are conserved across benzimidazole derivatives, but others show drug and dose specificity. We used near-isogenic lines to recapitulate and narrow the C. elegans albendazole QTL of largest effect and identified candidate variants correlated with the resistance phenotype. These QTL do not overlap with known benzimidazole target resistance genes from parasitic nematodes and present specific new leads for the discovery of novel mechanisms of nematode benzimidazole resistance. Analyses of orthologous genes reveal conservation of candidate benzimidazole resistance genes in medically important parasitic nematodes. These data provide a basis for extending these approaches to other anthelmintic drug classes and a pathway towards validating new markers for anthelmintic resistance that can be deployed to improve parasite disease control., Author summary The treatment of roundworm (nematode) infections in both humans and animals relies on a small number of anti-parasitic drugs. Resistance to these drugs has appeared in veterinary parasite populations and is a growing concern in human medicine. A better understanding of the genetic basis for parasite drug resistance can be used to help maintain the effectiveness of anti-parasitic drugs and to slow or to prevent the spread of drug resistance in parasite populations. This goal is hampered by the experimental intractability of nematode parasites. Here, we use non-parasitic model nematodes to systematically explore responses to the critical benzimidazole class of anti-parasitic compounds. Using a quantitative genetics approach, we discovered unique genomic intervals that control drug effects, and we identified differences in the effects of these intervals across compounds and doses. We were able to narrow a major-effect genomic region associated with albendazole resistance and to establish that candidate genes discovered in our genetic mappings are largely conserved in important human and animal parasites. This work provides new leads for understanding parasite drug resistance and contributes a powerful template that can be extended to other anti-parasitic drug classes.
- Published
- 2018
43. The Local Coexistence Pattern of Selfing Genotypes in
- Author
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Aurélien, Richaud, Gaotian, Zhang, Daehan, Lee, Junho, Lee, and Marie-Anne, Félix
- Subjects
Genome ,Polymorphism, Genetic ,Genotype ,2b-RAD ,fungi ,Genetic Variation ,Genomics ,Investigations ,colonization ,Genetics, Population ,Phenotype ,Haplotypes ,C . elegans ,selfing ,Animals ,Crossing Over, Genetic ,local populations ,Caenorhabditis elegans ,Population and Evolutionary Genetics ,Alleles ,Genes, Helminth - Abstract
To study the interplay of rare outcrossing and metapopulation structure, we focus on the nematode Caenorhabditis elegans. Its remarkably low outcrossing rate is at the extreme end of the spectrum for facultative selfing organisms. At the demographic level, C. elegans natural populations undergo boom and bust dynamics on ephemeral resources, with the dauer diapause larva acting as the dispersal form. Here we investigate the small-scale genetic structure of C. elegans populations in two localities over several years, using 2b restriction-associated DNA sequencing of nearly 1000 individuals. We find a remarkably small number of genome-wide haplotypes, almost exclusively in the homozygous state, confirming the low effective outcrossing rate. Most strikingly, the major haplotypes in a locality remain intact and do not effectively recombine over several years. From the spatial pattern of diversity, we estimate that each subpopulation or deme is seeded by a mean of 3–10 immigrating individuals. Populations are thus formed by clones that compete at two levels, within a subpopulation and at the metapopulation level. We test for the presence of local phenotypic variation in pathogen resistance and dauer larva nictation, which could possibly explain the maintenance of different genotypes by heterogeneous selection in different local environments or lifecycles. This study is the first to address the local spatiotemporal genetic structure of C. elegans on feeding substrates. We conclude that these animals coexist as competing homozygous clones at the smallest population scale as well as in the metapopulation.
- Published
- 2017
44. Discovery of unique loci that underlie nematode responses to benzimidazoles
- Author
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Daehan Lee, Shannon C. Brady, Junho Lee, Daniel E. Cook, Mostafa Zamanian, Erik C. Andersen, and Stefan Zdraljevic
- Subjects
Caenorhabditis briggsae ,Genetics ,0303 health sciences ,Benzimidazole ,biology ,030231 tropical medicine ,Quantitative trait locus ,biology.organism_classification ,Phenotype ,3. Good health ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Nematode ,chemistry ,medicine ,Anthelmintic ,Gene ,Caenorhabditis elegans ,030304 developmental biology ,medicine.drug - Abstract
Parasitic nematodes impose a debilitating health and economic burden across much of the world. Nematode resistance to anthelmintic drugs threatens parasite control efforts in both human and veterinary medicine. Despite this threat, the genetic landscape of potential resistance mechanisms to these critical drugs remains largely unexplored. Here, we exploit natural variation in the model nematodes Caenorhabditis elegans and Caenorhabditis briggsae to discover quantitative trait loci (QTL) that control sensitivity to benzimidazoles widely used in human and animal medicine. High-throughput phenotyping of albendazole, fenbendazole, mebendazole, and thiabendazole responses in panels of recombinant lines led to the discovery of over 15 QTL in C. elegans and four QTL in C. briggsae associated with divergent responses to these anthelmintics. Many of these QTL are conserved across benzimidazole derivatives, but others show drug and dose specificity. We used near-isogenic lines to recapitulate and narrow the C. elegans albendazole QTL of largest effect and identified candidate variants correlated with the resistance phenotype. These QTL do not overlap with known benzimidazole resistance genes from parasitic nematodes and present specific new leads for the discovery of novel mechanisms of nematode benzimidazole resistance. Analyses of orthologous genes reveal significant conservation of candidate benzimidazole resistance genes in medically important parasitic nematodes. These data provide a basis for extending these approaches to other anthelmintic drug classes and a pathway towards validating new markers for anthelmintic resistance that can be deployed to improve parasite disease control.Author SummaryThe treatment of roundworm (nematode) infections in both humans and animals relies on a small number of anti-parasitic drugs. Resistance to these drugs has appeared in veterinary parasite populations and is a growing concern in human medicine. A better understanding of the genetic basis for parasite drug resistance can be used to help maintain the effectiveness of anti-parasitic drugs and to slow or to prevent the spread of drug resistance in parasite populations. This goal is hampered by the experimental intractability of nematode parasites. Here, we use non-parasitic model nematodes to systematically explore responses to the critical benzimidazole class of anti-parasitic compounds. Using a quantitative genetics approach, we discovered unique genomic intervals that control drug effects, and we identified differences in the genetic architectures of drug responses across compounds and doses. We were able to narrow a major-effect genomic region associated with albendazole resistance and to establish that candidate genes discovered in our genetic mappings are largely conserved in important human and animal parasites. This work provides new leads for understanding parasite drug resistance and contributes a powerful template that can be extended to other anti-parasitic drug classes.
- Published
- 2017
45. The genetic basis of natural variation in a phoretic behavior
- Author
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Mostafa Zamanian, Heeseung Yang, Heekyeong Kim, Jun Kim, Leonid Kruglyak, Stefan Zdraljevic, Shannon C. Brady, Daehan Lee, Erik C. Andersen, Young Ki Paik, and Junho Lee
- Subjects
0301 basic medicine ,Small RNA ,Science ,General Physics and Astronomy ,Piwi-interacting RNA ,Locus (genetics) ,General Biochemistry, Genetics and Molecular Biology ,Article ,Host-Parasite Interactions ,03 medical and health sciences ,Isopoda ,Genetic linkage ,Animals ,RNA, Small Interfering ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,Symbiosis ,Genetics ,Multidisciplinary ,biology ,Behavior, Animal ,Chromosome Mapping ,General Chemistry ,Argonaute ,Commensalism ,biology.organism_classification ,030104 developmental biology ,Larva ,Argonaute Proteins ,Biological dispersal - Abstract
Phoresy is a widespread form of commensalism that facilitates dispersal of one species through an association with a more mobile second species. Dauer larvae of the nematode Caenorhabditis elegans exhibit a phoretic behavior called nictation, which could enable interactions with animals such as isopods or snails. Here, we show that natural C. elegans isolates differ in nictation. We use quantitative behavioral assays and linkage mapping to identify a genetic locus (nict-1) that mediates the phoretic interaction with terrestrial isopods. The nict-1 locus contains a Piwi-interacting small RNA (piRNA) cluster; we observe that the Piwi Argonaute PRG-1 is involved in the regulation of nictation. Additionally, this locus underlies a trade-off between offspring production and dispersal. Variation in the nict-1 locus contributes directly to differences in association between nematodes and terrestrial isopods in a laboratory assay. In summary, the piRNA-rich nict-1 locus could define a novel mechanism underlying phoretic interactions., Nematodes use a characteristic set of movements, called nictation, to hitchhike on more mobile animals. Here, Lee et al. identify a genetic locus in the nematode Caenorhabditis elegans that underlies nictation and contributes to successful hitchhiking, but at expense of reduced offspring production.
- Published
- 2016
46. Nictation, a dispersal behavior of the nematode Caenorhabditis elegans, is regulated by IL2 neurons
- Author
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Harksun Lee, Daehan Lee, Sungsu Park, Myung Kyu Choi, Hye Sung Kim, Heekyeong Kim, Junho Lee, Young Ki Paik, and Hyejin Hwang
- Subjects
Neurons ,Behavior, Animal ,Nematode caenorhabditis elegans ,General Neuroscience ,Cilium ,Cell ,Mutant ,Niche ,Biology ,Optogenetics ,Synaptic Transmission ,Acetylcholine ,stomatognathic diseases ,medicine.anatomical_structure ,medicine ,Animals ,Cholinergic ,Biological dispersal ,Cilia ,Caenorhabditis elegans ,Neuroscience - Abstract
Many nematodes show a stage-specific behavior called nictation in which a worm stands on its tail and waves its head in three dimensions. Here we show that nictation is a dispersal behavior regulated by a specific set of neurons, the IL2 cells, in C. elegans. We established assays for nictation and showed that cholinergic transmission was required for nictation. Cell type-specific rescue experiments and genetic ablation experiments revealed that the IL2 ciliated head neurons were essential for nictation. Intact cilia in IL2 neurons, but not in other ciliated head neurons, were essential, as the restoration of the corresponding wild-type gene activity in IL2 neurons alone in cilia-defective mutants was sufficient to restore nictation. Optogenetic activation of IL2 neurons induced nictation, suggesting that signals from IL2 neurons are sufficient for nictation. Finally, we demonstrated that nictation is required for transmission of C. elegans to a new niche using flies as artificial carriers, suggesting a role of nictation as a dispersal and survival strategy under harsh conditions.
- Published
- 2011
47. Nictation Assays for Caenorhabditis and Other Nematodes
- Author
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Myung-kyu Choi, Harksun Lee, Daehan Lee, Sungsu Park, and Junho Lee
- Subjects
Caenorhabditis ,Strategy and Management ,Mechanical Engineering ,Metals and Alloys ,Biology ,Behavioral neuroscience ,biology.organism_classification ,Neuroscience ,Industrial and Manufacturing Engineering - Published
- 2015
48. Erratum: Corrigendum: Nictation, a dispersal behavior of the nematode Caenorhabditis elegans, is regulated by IL2 neurons
- Author
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Young Ki Paik, Junho Lee, Daehan Lee, Hyejin Hwang, Hye Sung Kim, Heekyeong Kim, Harksun Lee, Myung Kyu Choi, and Sungsu Park
- Subjects
White (mutation) ,Nematode caenorhabditis elegans ,Ecology ,General Neuroscience ,Biological dispersal ,Zoology ,Biology ,Neuroscience - Abstract
Nat. Neurosci. 15, 107–112 (2012); published online 13 November 2011; corrected after print 10 August 2012 In the version of this article initially published, the average durations for N2, cha-1(n2411) and cha-1(p503) shown in Figure 2b (white bars) were incorrect because the n-values used to calculate them included cases in which no nictation was observed
- Published
- 2013
49. daf-42 is an evolutionarily young gene essential for dauer development in Caenorhabditis elegans.
- Author
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Lim, Daisy S., Jun Kim, Wonjoo Kim, Nari Kim, Sang-Hee Lee, Daehan Lee, and Junho Lee
- Subjects
- *
PROTEINS , *BIOLOGICAL evolution , *NEMATODES , *INSECT larvae , *GENETIC mutation , *CAENORHABDITIS elegans , *ANIMAL experimentation , *PLASMIDS , *GENES , *GENE expression profiling , *RESEARCH funding , *PHENOTYPES - Abstract
Under adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauer endures unfavorable environments and interacts with host animals to access favorable environments, thus playing a critical role in survival. Here, we report that in Caenorhabditis elegans, daf-42 is essential for development into the dauer stage, as the null mutant of daf-42 exhibited a "no viable dauer" phenotype in which no viable dauers were obtained in any dauer-inducing conditions. Long-term time lapse microscopy of synchronized larvae revealed that daf-42 is involved in developmental changes from the pre-dauer L2d stage to the dauer stage. daf-42 encodes large, disordered proteins of various sizes that are expressed in and secreted from the seam cells within a narrow time window shortly before the molt into dauer stage. Transcriptome analysis showed that the transcription of genes involved in larval physiology and dauer metabolism is highly affected by the daf-42 mutation. Contrary to the notion that essential genes that control the life and death of an organism may be well conserved across diverse species, daf-42 is an evolutionarily young gene conserved only in the Caenorhabditis genus. Our study shows that dauer formation is a vital process that is controlled not only by conserved genes but also by newly emerged genes, providing important insights into evolutionary mechanisms. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
50. A Novel Gene Underlies Bleomycin-Response Variation in Caenorhabditis elegans.
- Author
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Brady, Shannon C., Zdraljevic, Stefan, Bisaga, Karol W., Tanny, Robyn E., Cook, Daniel E., Daehan Lee, Ye Wang, and Andersen, Erik C.
- Subjects
- *
ALLELES , *ANIMAL experimentation , *BLEOMYCIN , *CELL lines , *CHROMOSOMES , *DRUG resistance , *GENE expression , *GENE mapping , *GENETIC polymorphisms , *GENETIC mutation , *NEMATODES , *PHYSIOLOGICAL stress , *GENOMICS - Abstract
Bleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organism Caenorhabditis elegans to identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain (N2) and a wild strain (CB4856). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines, and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene (scb-1) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function of scb-1 between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
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